TheSoulHarvester: I have a vague suspicion it may actually affect the prices of castle upgrades, but I could be way off the mark with that. I don't really understand how the levels work, despite being level 60-something.
Your level equals the number of manor upgrades, and the price of all other upgrades definitely does crank up each time you buy one.
I've tried wiping my save file a couple times and I'm pretty certain that when your level gets higher, higher numbers of enemies show up, higher level enemies show up (never see visionaries in the castle when you first start, at higher levels they're freaking everywhere), and chests spit out more money.
So it would seem the best strategy is to concentrate on buying runes and equipment first, and only THEN start cranking up the manor so the difficulty doesn't outpace you.